rename to rgi

.coveragerc

@@ -1,16 +1,16 @@
 [run]
-source=q2_amr
+source=q2_rgi
 branch = True
 omit =
     */tests*
     */__init__.py
-    q2_amr/_version.py
+    q2_rgi/_version.py
     versioneer.py
 
 [report]
 fail_under = 90
 omit =
     */tests*
     */__init__.py
-    q2_amr/_version.py
+    q2_rgi/_version.py
     versioneer.py

.gitattributes

@@ -1 +1 @@
-q2_amr/_version.py export-subst
+q2_rgi/_version.py export-subst

.gitignore

@@ -131,6 +131,6 @@ dmypy.json
 
 # PyCharm configuration
 .idea/
-/q2_amr/charts_testing.py
+/q2_rgi/charts_testing.py
 /index.html
 /bwt_test_file.py

MANIFEST.in

@@ -1,2 +1,2 @@
 include versioneer.py
-include q2_amr/_version.py
+include q2_rgi/_version.py

README.md

@@ -1,27 +1,27 @@
-# q2-amr
-![CI](https://github.com/bokulich-lab/q2-amr/actions/workflows/ci-dev.yaml/badge.svg)
-[![codecov](https://codecov.io/gh/bokulich-lab/q2-amr/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-amr)
+# q2-rgi
+![CI](https://github.com/bokulich-lab/q2-rgi/actions/workflows/ci-dev.yaml/badge.svg)
+[![codecov](https://codecov.io/gh/bokulich-lab/q2-rgi/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-rgi)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.
 
 ## Installation
-To install _q2-amr_, follow the steps described below.
+To install _q2-rgi_, follow the steps described below.
 
 <details>
 <summary><b>macOS (intel) / Linux</b></summary>
 
 ```shell
-mamba create -yn q2-amr \
+mamba create -yn q2-rgi \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
   qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
 
-conda activate q2-amr
+conda activate q2-rgi
 
 pip install --no-deps --force-reinstall \
   git+https://github.com/misialq/rgi.git@py38-fix \
-  git+https://github.com/bokulich-lab/q2-amr.git
+  git+https://github.com/bokulich-lab/q2-rgi.git
 ```
 
 Refresh cache and check that everything worked:
@@ -35,17 +35,17 @@ qiime info
 <summary><b>macOS (apple silicon)</b></summary>
 
 ```shell
-CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
+CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
   qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
 
-conda activate q2-amr
+conda activate q2-rgi
 conda config --env --set subdir osx-64
 
 pip install --no-deps --force-reinstall \
   git+https://github.com/misialq/rgi.git@py38-fix \
-  git+https://github.com/bokulich-lab/q2-amr.git
+  git+https://github.com/bokulich-lab/q2-rgi.git
 ```
 
 Refresh cache and check that everything worked:

ci/recipe/meta.yaml

@@ -2,7 +2,7 @@
 {% set version = data.get('version') or 'placehold' %}
 
 package:
-  name: q2-amr
+  name: q2-rgi
   version: {{ version }}
 
 source:
@@ -32,12 +32,12 @@ test:
     - coverage
     - pytest-cov
   imports:
-    - q2_amr
+    - q2_rgi
     - qiime2.plugins.amr
   commands:
-    - pytest --cov q2_amr --cov-report xml:coverage.xml --pyargs q2_amr
+    - pytest --cov q2_rgi --cov-report xml:coverage.xml --pyargs q2_rgi
 
 about:
-  home: https://github.com/bokulich-lab/q2-amr
+  home: https://github.com/bokulich-lab/q2-rgi
   license: BSD-3-Clause
   license_family: BSD